JMIH 2026 – Danielle Rivera

Here is an expanded version of the poster with more figures from the manuscript:

Rivera D, Arocho-Hernandez N, Zegarra JP, Rivenbark E, Chovanec KR, Reynolds RG, de Queiroz K, Hedges SB, Puente-Rolón AR, Gonzalez-Arocho L, Hostetter NJ, Collazo JA, Bell RC. 2026. Genomic data reveal historical introgression and genetic erosion across an imperiled radiation of Caribbean Spondylurus skinks. Evolutionary Journal of the Linnean Society. In Review.

References in this Manuscript

  1. Ali JR, Hedges SB. 2024. Paleogeography of the Aves Ridge and its potential role as a bio-colonization pathway linking South America and the Greater Antilles in the mid-Cenozoic. Earth-Science Reviews 254: 104823.
  2. Allendorf FW, Leary RF, Spruell P, Wenburg JK. 2001. The problems with hybrids: setting conservation guidelines. Trends in Ecology & Evolution 16: 613–622.
  3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.
  4. Ballard JWO, Whitlock MC. 2004. The incomplete natural history of mitochondria. Molecular Ecology 13: 729–744.
  5. Battilani D, Gargiulo R, Caniglia R, Fabbri E, Madrigal JR, Fontsere C, Ciucani MM, Gopalakrishnan S, Girardi M, Fracasso I, Mastroiaco M, Ciucci P, Vernesi C. 2025. Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf. The Journal of Heredity 116: 10–23.
  6. Bell RC, Parra JL, Badjedjea G, Barej MF, Blackburn DC, Burger M, Channing A, Dehling JM, Greenbaum E, Gvoždík V, Kielgast J, Kusamba C, Lötters S, McLaughlin PJ, Nagy ZT, Rödel MO, Portik DM, Stuart BL, VanDerWal J, Zassi-Boulou AG, Zamudio KR. 2017. Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands. Molecular Ecology 26: 5223–5244.
  7. Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69: 313–319.
  8. Bertorelle G, Raffini F, Bosse M, Bortoluzzi C, Iannucci A, Trucchi E, Morales HE, van Oosterhout C. 2022. Genetic load: genomic estimates and applications in non-model animals. Nature reviews. Genetics 23: 492–503.
  9. Biscarini F, Cozzi P, Gaspa G, Marras G. 2018. detectRUNS: Detect runs of homozygosity and runs of heterozygosity in diploid genomes.
  10. Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ. 2019. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology 15: e1006650.
  11. Broman KW, Weber JL. 1999. Long homozygous chromosomal segments in reference families from the centre d’Etude du polymorphisme humain. American Journal of Human Genetics 65: 1493–1500.
  12. Brown RM, Diesmos AC. 2002. Application of lianeage-based species concepts to oceanic island frog populations: The effects of differing taxonomic philosophies on the estimation of Philippine biodiversity. Silliman Journal 42: 133–162.
  13. Bryant D, Moulton V. 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution 21: 255–265.
  14. Čandek K, Agnarsson I, Binford GJ, Kuntner M. 2021. Biogeography of long-jawed spiders reveals multiple colonization of the Caribbean. Diversity 13: 622.
  15. Cavill EL, Morales HE, Sun X, Westbury MV, van Oosterhout C, Accouche W, Zora A, Schulze MJ, Shah N, Adam PA, Brooke M de L, Sweet P, Gopalakrishnan S, Gilbert MTP. 2024. When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine. Evolutionary Applications 17: e13739.
  16. Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. 2018. Runs of homozygosity: windows into population history and trait architecture. Nature reviews. Genetics 19: 220–234.
  17. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4: 7.
  18. Chen S. 2023. Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2.
  19. Chen Y, Feng X, Reid K, Zhang C, Löytynoja A, Merilä J. 2025. Dynamics of deleterious mutations and purifying selection in small population isolates. Molecular Biology and Evolution 42.
  20. Chifman J, Kubatko L. 2015. Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. Journal of Theoretical Biology 374: 35–47.
  21. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6: 80–92.
  22. Crews SC, Esposito LA. 2020. Towards a synthesis of the Caribbean biogeography of terrestrial arthropods. BMC Evolutionary Biology 20: 12.
  23. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group. 2011. The variant call format and VCFtools. Bioinformatics (Oxford, England) 27: 2156–2158.
  24. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10.
  25. Daza JD, Pinto BJ, Thomas R, Herrera-Martinez A, Scantlebury DP, García LFP, Balaraman RP, Perry G, Gamble T. 2019. The sprightly little sphaerodactyl: Systematics and biogeography of the Puerto Rican dwarf geckos Sphaerodactylus (Gekkota, Sphaerodactylidae). Zootaxa 4712: zootaxa.4712.2.1.
  26. Díez-Del-Molino D, Sánchez-Barreiro F, Barnes I, Gilbert MTP, Dalén L. 2018. Quantifying temporal genomic erosion in endangered species. Trends in Ecology & Evolution 33: 176–185.
  27. Dussex N, Morales HE, Grossen C, Dalén L, van Oosterhout C. 2023. Purging and accumulation of genetic load in conservation. Trends in Ecology & Evolution 38: 961–969.
  28. Edelman NB, Mallet J. 2021. Prevalence and adaptive impact of introgression. Annual Review of Genetics 55: 265–283.
  29. Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, Glenn TC, Zhong B, Wu S, Lemmon EM, Lemmon AR, Leaché AD, Liu L, Davis CC. 2016. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Molecular Phylogenetics and Evolution 94: 447–462.
  30. Elliot MG, Crespi BJ. 2006. Placental invasiveness mediates the evolution of hybrid inviability in mammals. The American Naturalist 168: 114–120.
  31. Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW Jr, Ferri-Yáñez F, Leaché AD. 2022. Rapid radiation and rampant reticulation: phylogenomics of South American Liolaemus lizards. Systematic Biology 71: 286–300.
  32. Fernández-Palacios JM, Kreft H, Irl SDH, Norder S, Ah-Peng C, Borges PAV, Burns KC, de Nascimento L, Meyer JY, Montes E, Drake DR. 2021. Scientists’ warning – The outstanding biodiversity of islands is in peril. Global Ecology and Conservation 31: e01847.
  33. Fitak RR. 2021. OptM: estimating the optimal number of migration edges on population trees using Treemix. Biology Methods & Protocols 6: bpab017.
  34. Fitzgerald LA, Treglia ML, Angeli N, Hibbitts TJ, Leavitt DJ, Subalusky AL, Lundgren I, Hillis-Starr Z. 2015. Determinants of successful establishment and post‐translocation dispersal of a new population of the critically endangered St. Croix ground lizard ( Ameiva polops ): Correlates to successful translocation. Restoration Ecology 23: 776–786.
  35. Fitzpatrick SW, Funk WC. 2019. Genomics for genetic rescue. Population Genomics. Cham: Springer International Publishing, 437–471.
  36. Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. 2021. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (Bethesda, Md.) 11.
  37. Frankham R, Ballou JD, Ralls K, Eldridge M, Dubash MR, Fenster CB, Lacy RC, Sunnucks P. 2017. Genetic management of fragmented animal and plant populations. London, England: Oxford University Press.
  38. Gabrielli M, Benazzo A, Biello R, Iannucci A, Salvi D, Ficetola GF, Ciofi C, Trucchi E, Bertorelle G. 2026. The relationship between genomic variation and genetic load: insights from small island populations. Heredity 135: 332–341.
  39. García-Dorado A. 2012. Understanding and predicting the fitness decline of shrunk populations: inbreeding, purging, mutation, and standard selection. Genetics 190: 1461–1476.
  40. Gyllenhaal EF, Klicka LB, DeCicco LH, Weeks BC, Moyle RG, Andersen MJ. 2025. Gene flow complicates phylogenetic inference in an archipelago radiation. Systematic Biology.
  41. Heaney LR. 1985. Zoogeographic evidence for middle and upper Pleistocene land bridges to the Philippine islands. Indo-Pacific Prehistory Association Philippines. Congress.127–143.
  42. Heaney LR. 1986. Biogeography of mammals in SE Asia: estimates of rates of colonization, extinction and speciation. Biological Journal of the Linnean Society. Linnean Society of London 28: 127–165.
  43. Heatwole H. 1968. Herpetogeography of Puerto Rico. V. Description of a new species of Sphaerodactylus from Desecheo Island. Breviora: 1–6.
  44. Heatwole H. 1976. Herpetogeography of Puerto Rico. VII. Geographic variation in the Anolis cristatellus complex in Puerto Rico and the Virgin Islands. Occasional Papers of the Natural History Museum, the University of Kansas, Lawrence, Kansas 46: 1–17.
  45. Heatwole H, Torres F. 1967. Distribution and geographic variation of the Ameivas of Puerto Rico and the Virgin Islands. Stud. Fauna Curaçao and Carib. Is 24: 63–64.
  46. Hedges SB, Conn CE. 2012. A new skink fauna from Caribbean islands (Squamata, Mabuyidae, Mabuyinae). Zootaxa 3288: 1.
  47. Hedrick PW, Kalinowski ST. 2000. Inbreeding depression in conservation biology. Annual Review of Ecology and Systematics 31: 139–162.
  48. Heinicke MP, Duellman WE, Hedges SB. 2007. Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal. Proceedings of the National Academy of Sciences of the United States of America 104: 10092–10097.
  49. Hibbins MS, Hahn MW. 2022. Phylogenomic approaches to detecting and characterizing introgression. Genetics 220.
  50. Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. 2018. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35: 518–522.
  51. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254–267.
  52. Huson DH, Bryant D. 2024. The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks. Nature Methods 21: 1773–1774.
  53. Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF. 2012. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Research 40: 2833–2845.
  54. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14: 587–589.
  55. Kardos M, Waples RS. 2025. Low-coverage sequencing and Wahlund effect severely bias estimates of inbreeding, heterozygosity and effective population size in North American wolves. Molecular Ecology 34: e17415.
  56. Katoh K, Misawa K, Kuma KI, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059–3066.
  57. Khan A, Patel K, Shukla H, Viswanathan A, van der Valk T, Borthakur U, Nigam P, Zachariah A, Jhala YV, Kardos M, Ramakrishnan U. 2021. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proceedings of the National Academy of Sciences of the United States of America 118: e2023018118.
  58. Knaus BJ, Grünwald NJ. 2016. VcfR: a package to manipulate and visualize VCF format data in R. bioRxiv.
  59. Knaus BJ, Grünwald NJ. 2017. vcfr: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources 17: 44–53.
  60. Knowles LL, Carstens BC. 2007. Delimiting species without monophyletic gene trees. Systematic Biology 56: 887–895.
  61. Korunes KL, Samuk K. 2021. pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Molecular Ecology Resources 21: 1359–1368.
  62. Lambert SM, Geneva AJ, Luke Mahler D, Glor RE. 2013. Using genomic data to revisit an early example of reproductive character displacement in Haitian Anolis lizards. Molecular Ecology 22: 3981–3995.
  63. Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L. 2015. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518: 371–375.
  64. Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular biology and evolution 29: 1695–1701.
  65. Lavanchy E, Goudet J. 2023. Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization. Molecular Ecology Resources 23: 787–802.
  66. Leroy G, Carroll EL, Bruford MW, DeWoody JA, Strand A, Waits L, Wang J. 2018. Next-generation metrics for monitoring genetic erosion within populations of conservation concern. Evolutionary Applications 11: 1066–1083.
  67. Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN].
  68. Li D, Liu CM, Luo R, Sadakane K, Lam TW. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31: 1674–1676.
  69. Liu L, Edwards SV. 2009. Phylogenetic analysis in the anomaly zone. Systematic Biology 58: 452–460.
  70. Long C, Kubatko L. 2018. The effect of gene flow on coalescent-based species-tree inference. Systematic Biology 67: 770–785.
  71. Losos JB, Ricklefs RE. 2009. Adaptation and diversification on islands. Nature 457: 830–836.
  72. Maddison WP, Knowles LL. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55: 21–30.
  73. Mathur S, Gibbs HL. 2025. Genomic evaluation of assisted gene flow options in an endangered rattlesnake. Molecular Ecology 34: e70014.
  74. Mathur S, & DeWoody JA. 2021. Genetic load has potential in large populations but is realized in small inbred populations. Evolutionary Applications 14(6): 1540–1557.
  75. Meyermans R, Gorssen W, Buys N, Janssens S. 2020. How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species. BMC Genomics 21: 94.
  76. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution 37: 1530–1534.
  77. Montheil L, van Hinsbergen DJJ, Philippon M. et al. 2025. Caribbean biodiversity shaped by subduction zone processes along the Lesser Antilles arch. Commun Earth Environ 6: 900.
  78. Morrison KR, Zúñiga-Vega JJ, Travis J, Reznick DN. 2025. The evolution of a placenta accelerates the evolution of postcopulatory reproductive isolation. Evolution; International Journal of Organic Evolution 79: 457–466.
  79. Myers EA, Mulcahy DG, Falk B, Johnson K, Carbi M, de Queiroz K. 2022. Interspecific gene flow and mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae). Systematic Biology 71: 501–511.
  80. Nieto-Blázquez ME, Antonelli A, Roncal J. 2017. Historical Biogeography of endemic seed plant genera in the Caribbean: Did GAARlandia play a role? Ecology and Evolution 7: 10158–10174.
  81. van Oosterhout C. 2020. Mutation load is the spectre of species conservation. Nature Ecology & Evolution 4: 1004–1006.
  82. Ortiz EM. 2019. vcf2phylip v2.0: convert a VCF matrix into several matrix formats for phylogenetic analysis.
  83. Ortiz MA, Boretto JM, Ibargüengoytía NR. 2019. Reproductive biology of a viviparous lizard (Mabuya dorsivittata) from the subtropical Wet Chaco of Argentina: geographical variations in response to local environmental pressures. Anais da Academia Brasileira de Ciencias 91: e20170817.
  84. Papadopoulou A, Knowles LL. 2015. Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands. Evolution; International Journal of Organic Evolution 69: 1501–1517.
  85. Parham JF, Papenfuss TJ, van Dijk PP, Wilson BS, Marte C, Schettino LR, Brian Simison W. 2013. Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers. Molecular Phylogenetics and Evolution 67: 176–187.
  86. Pascarella JB, Aide TM, Serrano MI, Zimmerman JK. 2000. Land-use history and forest regeneration in the Cayey mountains, Puerto Rico. Ecosystems (New York, N.Y.) 3: 217–228.
  87. Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. 2012. Genomic patterns of homozygosity in worldwide human populations. American Journal of Human Genetics 91: 275–292.
  88. Philibosian R, Ruibal R. 1971. Conservation of the lizard Ameiva polops in the Virgin Islands. Herpetologica 27: 450–454.
  89. Pickrell JK, Pritchard JK. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics 8: e1002967.
  90. Pindell JL, Kennan L. 2009. Tectonic evolution of the Gulf of Mexico, Caribbean and northern South America in the mantle reference frame: an update. Geological Society Special Publication 328: 1–55.
  91. Poe S, Nieto-Montes de Oca A, Torres-Carvajal O, De Queiroz K, Velasco JA, Truett B, Gray LN, Ryan MJ, Köhler G, Ayala-Varela F, Latella I. 2017. A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae). Systematic Biology 66: 663–697.
  92. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81: 559–575.
  93. Purfield DC, McParland S, Wall E, Berry DP. 2017. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PloS One 12: e0176780.
  94. Questel, K. 2009. Spondylurus powelli observation.iNaturalist, observation 192744545. Available at https://www.inaturalist.org/observations/192744545. Accessed 01 Dec 2025.
  95. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Systematic Biology 67: 901–904.
  96. Ramírez-Pinilla MP, Serrano VH, Galeano JC, Ramirez-Pinilla MP, Serrano VH. 2002. Annual Reproductive Activity of Mabuya mabouya (Squamata, Scincidae). Journal of Herpetology 36: 667.
  97. Reed TE, Kane A, McGinnity P, O’Sullivan RJ. 2024. Competitive interactions affect introgression and population viability amidst maladaptive hybridization. Evolutionary Applications 17: e13746.
  98. Reynolds G, Comsa C, Niemiller M. 2024. Status and observations of the critically endangered Turks Island Skink (Spondylurus turksae). Reptiles & Amphibians 31: e22449–e22449.
  99. Reynolds RG, Strickland TR, Kolbe JJ, Falk BG, Perry G, Revell LJ, Losos JB. 2017. Archipelagic genetics in a widespread Caribbean anole. Journal of Biogeography 44: 2631–2647.
  100. Rhymer JM, Simberloff D. 1996. Extinction by hybridization and introgression. Annual Review of Ecology and Systematics 27: 83–109.
  101. Richmond JQ, Jockusch EL, Latimer AM. 2011. Mechanical reproductive isolation facilitates parallel speciation in western North American scincid lizards. The American Naturalist 178: 320–332.
  102. Rivera D, Henderson JB, Lam AW, Hostetter NJ, Collazo JA, Bell RC. 2024. High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks Spondylurus nitidus and S. culebrae. Genome Biology and Evolution.
  103. Rivera D, Arocho-Hernandez N, Zegarra JP, Rivenbark E, Chovanec KR, Reynolds RG, de Queiroz K, Hedges SB, Puente-Rolón AR, Gonzalez-Arocho L, Hostetter N, Collazo J, Bell R. 2026. Data from: Genomic data reveal historical introgression and genetic erosion across an imperiled radiation of Caribbean Spondylurus skinks. https://doi.org/10.5281/zenodo.18615513.
  104. Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. 2023. Deleterious variation in natural populations and implications for conservation genetics. Annual Review of Animal Biosciences 11: 93–114.
  105. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542.
  106. Ruane S, Austin CC. 2017. Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens. Molecular Ecology Resources 17: 1003–1008.
  107. Santiago E, Köpke C, Caballero A. 2025. Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods. Nature Communications 16: 6054.
  108. Santiago E, Novo I, Pardiñas AF, Saura M, Wang J, Caballero A. 2020. Recent demographic history inferred by high-resolution analysis of linkage disequilibrium. Molecular Biology and Evolution 37: 3642–3653.
  109. Smeds L, Ellegren H. 2023. From high masked to high realized genetic load in inbred Scandinavian wolves. Molecular Ecology 32: 1567–1580.
  110. Smith, R. H. 2021. Spondylurus anegadae observation. iNaturalist, observation 91495795. Available at https://www.inaturalist.org/observations/91495795. Accessed 01 Dec 2025. 
  111. Streicher JW, Schulte JA 2nd, Wiens JJ. 2016. How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards. Systematic Biology 65: 128–145.
  112. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus evolution 4: vey016.
  113. Swofford DL. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates.
  114. Tershy BR, Shen KW, Newton KM, Holmes ND, Croll DA. 2015. The importance of islands for the protection of biological and linguistic diversity. Bioscience 65: 592–597.
  115. Thomas R, Schwartz A. 1966. Sphaerodactylus (Gekkonidae) in the greater Puerto Rico region. Bulletin of the Florida State Museum. Biological Sciences 10: 193–260.
  116. Torres J. 2025. A revision of the Anolis carolinensis subgroup supports three species in Cuba, including a new cryptic species (Squamata: Anolidae). Vertebrate Zoology 75: 107–126.
  117. Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. 2016. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44: W232–5.
  118. Tucker DB, Hedges SB, Colli GR, Pyron RA, Sites JW Jr. 2017. Genomic timetree and historical biogeography of Caribbean island ameiva lizards (Pholidoscelis: Teiidae). Ecology and Evolution 7: 7080–7090.
  119. Turner TL, Hahn MW. 2010. Genomic islands of speciation or genomic islands and speciation? Molecular Ecology 19: 848–850.
  120. U.S. Fish and Wildlife Service. 2023. Species status assessment report for eight Caribbean skinks: Puerto Rican skink (Spondylurus nitidus), Mona skink (S. monae), Culebra skink (S. culebrae), Greater Virgin Islands skink (S. spilonotus), Lesser Virgin Islands skink (S. semitaeniatus), Virgin Islands bronze skink (S. sloanii), Greater St. Croix skink (S. magnacruzae), and Lesser St. Croix skink (Capitellum parvicruzae). Atlanta, GA: U.S. Fish and Wildlife Service, Southeast Region.
  121. U.S. Fish and Wildlife Service. 2024. Endangered and Threatened Wildlife and Plants; Endangered Species Status for Puerto Rican Skink, Lesser Virgin Islands Skink, and Virgin Islands Bronze Skink and Designation of Critical Habitat; Threatened Species Status With Section 4(d) Rule for Culebra Skink and Designation of Critical Habitat; Not Warranted Species Status for Mona Skink, Greater Virgin Islands Skink, Greater Saint Croix Skink, and Lesser Saint Croix Skink. 89: 103938–103989.
  122. van der Valk T, Díez-Del-Molino D, Marques-Bonet T, Guschanski K, Dalén L. 2019. Historical genomes reveal the genomic consequences of recent population decline in eastern gorillas. Current Biology 29: 165–170.e6.
  123. Veltjen E, Testé E, Palmarola Bejerano A, Asselman P, Hernández Rodríguez M, Roberto González Torres L, Chatrou LW, Goetghebeur P, Larridon I, Samain MS. 2022. The evolutionary history of the Caribbean magnolias (Magnoliaceae): Testing species delimitations and biogeographical hypotheses using molecular data. Molecular Phylogenetics and Evolution 167: 107359.
  124. Vitt LJ, Blackburn DG. 1991. Ecology and life history of the viviparous lizard Mabuya bistriata (scincidae) in the Brazilian Amazon. Copeia 1991: 916.
  125. Vlček J, Espinoza-Ulloa S, Cowles SA, Ortiz-Catedral L, Coutu C, Chaves JA, Andrés J, Štefka J. 2025. Genomes of Galápagos mockingbirds reveal the impact of island size and past demography on inbreeding and genetic load in contemporary populations. Molecular Ecology 34: e17665.
  126. Wang S, Zhu W, Gao X, Li X, Yan S, Liu X, Yang J, Gao Z, Li Y. 2014. Population size and time since island isolation determine genetic diversity loss in insular frog populations. Molecular Ecology 23: 637–648.
  127. Warren BH, Simberloff D, Ricklefs RE, Aguilée R, Condamine FL, Gravel D, Morlon H, Mouquet N, Rosindell J, Casquet J, Conti E, Cornuault J, Fernández-Palacios JM, Hengl T, Norder SJ, Rijsdijk KF, Sanmartín I, Strasberg D, Triantis KA, Valente LM, Whittaker RJ, Gillespie RG, Emerson BC, Thébaud C. 2015. Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson. Ecology Letters 18: 200–217.
  128. Whittaker R. 2006. Island biogeography: Ecology, evolution, and conservation. Oxford biology. Cary, NC: Oxford University Press.Yang W, Feiner N, Laakkonen H, Sacchi R, Zuffi MAL, Scali S, While GM, Uller T. 2020. Spatial variation in gene flow across a hybrid zone reveals causes of reproductive isolation and asymmetric introgression in wall lizards. Evolution; International Journal of Organic Evolution 74: 1289–1300.